神经科学

Neuroinflammation disrupts blood–brain barrier (BBB) integrity, promoting leukocyte recruitment into the central nervous system and contributing to the progression of neurological disorders. This protocol describes a reproducible macrophage adhesion assay to evaluate interactions between immune cells and brain endothelial cells and to screen compounds with potential anti-inflammatory activity. Murine brain endothelial cells (bEnd.3) were cultured to confluency and exposed to inflammatory stimuli, such as lipopolysaccharide (LPS) or pilocarpine, a cholinergic muscarinic receptor agonist reported to induce inflammatory responses through seizure-associated neuroinflammatory mechanisms, in the presence or absence of candidate therapeutic compounds. In these studies, the natural flavonoid quercetin and the synthetic alkyl-lysophospholipid edelfosine were tested for their effects on macrophage adhesion. After 48 h of treatment, fluorescently labeled murine macrophages (RAW 264.7) were added to the endothelial monolayer, and adherent cells were quantified by fluorescence microscopy. The assay was validated using dexamethasone as an anti-inflammatory control and inflammatory stimulation with LPS or pilocarpine. As expected, dexamethasone reduced macrophage adhesion, whereas both LPS and pilocarpine significantly increased adhesion, demonstrating the assay's sensitivity to changes in endothelial inflammatory status. Overall, this protocol provides a reliable and accessible platform for investigating endothelial–immune cell interactions under neuroinflammatory conditions and for evaluating therapeutic compounds that may preserve BBB function and reduce inflammatory cell recruitment in neurological disease models.

Cytoplasmic protein aggregation is a defining feature of multiple neurodegenerative diseases, including amyotrophic lateral sclerosis, frontotemporal dementia, Huntington’s disease, and certain forms of motor neuron disease. Recent evidence indicates that promyelocytic leukemia protein (PML) and engineered PML-derived variants can act as versatile aggregate-remodeling factors. In particular, cytoplasmically redirected PML variants recognize pathological cytoplasmic inclusions and promote their clearance. Here, we describe a protocol to generate and validate two engineered cytoplasmic PML variants: full-length mPML, which is redirected to the cytoplasm by disruption of its nuclear localization sequence, and the truncated mPML^ΔRBC variant, which lacks the RING, B-box, and coiled-coil domain but retains aggregate-reducing activity. The protocol integrates fluorescence-based imaging, bimolecular fluorescence complementation, detergent-soluble/insoluble fractionation, and validation in primary rat cortical neurons. This workflow provides a practical platform for assessing cytoplasmic aggregate burden and for comparing the aggregate-remodeling activities of PML-derived constructs. It can also be adapted to other disease-associated aggregation-prone proteins, including TDP-43, SOD1, FUS, tau, polyGA, and polyQ-expanded proteins.

Amyotrophic lateral sclerosis (ALS) is characterized by early and spatially restricted pathology in motor axons, including distal degeneration and accumulation of aggregation-prone proteins such as TDP-43. However, a major limitation in the field has been the lack of approaches that enable robust, quantitative, and compartment-specific analysis of these early axonal events, particularly in human-relevant systems. Here, we describe an integrated experimental and analytical framework that enables quantitative dissection of axonal degeneration and protein aggregation, specifically within distal motor axons. By combining compartmentalized human co-cultures with a dedicated image analysis strategy, this approach enables selective and quantitative analysis of pathological processes specifically within axons, independent of surrounding tissues such as muscle and other cellular compartments. This framework captures both structural degeneration and protein aggregation dynamics at subcellular resolution, enabling spatially resolved quantitative analysis of disease-relevant changes along axons. Importantly, the analytical framework is not limited to TDP-43 but is broadly applicable to diverse aggregation-prone proteins, thereby providing a generalizable platform to study axonal pathology across neurodegenerative diseases. Together, this work provides a scalable approach for investigating axonal pathology as an early and measurable feature of neurodegeneration, with potential applications in mechanistic studies and therapeutic targeting in ALS and related disorders.

Acid ceramidase (aCDase) is a lysosomal amidase that catalyzes the hydrolysis of sphingolipids (SphL), including ceramides and glucosylceramides. Altered expressions of aCDase are associated with several pathological conditions, such as cancer, inflammation, pain, and pulmonary disorders. aCDase activity is reduced in Farber disease, spinal muscular atrophy with progressive myoclonic epilepsy, diabetes, and cardiovascular disease. Recent reports suggest that aCDase inhibition may be an emerging strategy for treating several SphL-related neurodegenerative conditions, such as Krabbe, Gaucher, and Parkinson’s disease, due to its role in the accumulation of glycosphingolipids. Therefore, the development of a tissue-based aCDase activity assay has potential applications in clinical diagnostics and drug discovery, enabling the evaluation of the onset and progression of disease from biological samples of patients, drug-target engagement analysis, and identification of biomarkers. Here, we report a detailed protocol for detecting aCDase activity in tissue lysates, using Rbm14-12 as a specific fluorogenic substrate for aCDase. Assay protocol optimization, including a procedure for the preparation and storage of tissue lysates and the identification of optimal protein tissue lysate amounts and substrate concentrations based on kinetic enzymatic parameter analyses, is described.

Progressive neurodegeneration linked to the accumulation of misfolded proteins is a hallmark of several neurodegenerative disorders, including Parkinson’s disease, Huntington’s disease, and Alzheimer’s disease. Dysfunction in the protein homeostasis machinery correlates with pathology. The chaperone protein DNAJB6 is expressed in neurons and oligodendrocytes and has been shown to play a key role in preventing amyloid aggregation by binding to amyloidogenic proteins and facilitating their refolding or degradation, in cooperation with other chaperones. Here, we describe a simple and feasible assay that enables high-throughput screening for DNAJB6 activity in a plate reader format. We use genetically engineered HEK293 cells that stably express DNAJB6 fused to either CFP or YFP. These cells can be plated into multi-well plates, and the fluorescence resonance energy transfer (FRET) signal can be measured for analysis of DNAJB6 dimerization, which is linked to DNAJB6 activity. The protocol can be used for drug screening and to identify compounds that increase DNAJB6 dimerization, and can serve as a starting point for finding new medicines that act through modulating DNAJB6 activity.

α-Synuclein (α-syn) aggregation has emerged as a key pathogenetic feature in several neurodegenerative disorders. The α-syn protein has various conformational strains, each with unique structural features that influence their cytotoxicity, propagation, and neuroinflammation. A post-translational modification known as O-GlcNAcylation has been found to influence the toxicity of α-syn and its propensity to aggregate. Difficulties in detecting and quantifying this modification are a major challenge to understanding its roles among the conformational forms of α-syn. We now describe a protocol for detecting O-GlcNAcylated α-syn that combines a click chemistry labeling approach and western blotting. This chemoenzymatic method involves the transfer of azido-modified galactose (GalNAz) from UDP-GalNAz to O-GlcNAcylated proteins, enabling their further functionalization with alkyne-containing polyethylene glycol of defined molecular weight. This protocol facilitates the determination of the glycosylation status of varying conformations of α-syn and their stoichiometric ratios.

Experimental autoimmune encephalomyelitis (EAE) is a widely used rodent model of multiple sclerosis (MS), typically induced with pertussis toxin (PTX) to achieve robust disease onset. However, PTX has been shown to exert broad immunomodulatory effects that include disruption of G protein-coupled receptor (GPCR) signaling, altered T-cell response, and exogenous suppression of regulatory T cells, all of which are not present in human MS pathophysiology. Moreover, PTX also obscures the sex differences observed in MS, limiting the translational value of EAE models that rely on it. Given EAE’s widespread use in preclinical therapeutic testing, there is a critical need for a model that better recapitulates both clinical and immunological features of MS without PTX-induced confounds. Here, we demonstrate a non-pertussis toxin (non-PTX) EAE model in C57BL/6 mice, using optimized concentrations of complete Freund’s adjuvant (CFA), Mycobacterium tuberculosis, and myelin oligodendrocyte glycoprotein (MOG_35-55) peptide. This model recapitulates hallmark features of MS that include demyelination, neuroinflammation, motor deficits, and neuropathic pain. Importantly, it retains sex-specific differences in disease onset and pathology, providing a more physiologically and clinically relevant platform for mechanistic and translational MS research.

This protocol describes a reproducible workflow for modeling in vitro impact-induced traumatic brain injury (TBI) using a mechanical stretch system applied to differentiated SH-SY5Y human neuroblastoma cells cultured on polydimethylsiloxane (PDMS) substrates. The protocol integrates three primary components: (1) fabrication and surface modification of deformable PDMS chambers to support cellular adhesion, (2) partial differentiation of SH-SY5Y cells using retinoic acid, and (3) induction of controlled mechanical strain to simulate mild to moderate TBI. The stretch-induced injury model enables quantitative assessment of cellular viability and recovery following mechanical insult. This approach provides a versatile platform for studying cellular and molecular mechanisms of TBI, screening neuroprotective compounds, and exploring mechanobiological responses in neural cells under controlled strain magnitudes and rates.

Characterizing the morphology of amyloid proteins is an integral part of studying neurodegenerative diseases. Such morphological characterization can be performed using atomic force microscopy (AFM), which provides high-resolution images of the amyloid protein fibrils. AFM is widely employed for visualizing mechanical and physical properties of amyloid fibrils, not only from a biological and medical perspective but also in relation to their nanotechnological applications. A crucial step in AFM imaging is coating the protein of interest onto a substrate such as mica. However, existing protocols for this process vary considerably. The conventional sample preparation method often introduces artifacts, particularly due to deposition of excess salt. Hence, an optimized protocol is essential to minimize salt aggregation on the mica surface. Here, we present an optimized protocol for coating amyloid proteins onto mica using the dip-washing method to eliminate background noise. This approach improves the adherence of protein to the mica surface while effectively removing residual salts.

Microglia, the resident immune cells of the central nervous system, play a crucial role in maintaining neural homeostasis and in regulating neurodevelopment, neuroinflammation, tissue repair, and neurotoxicity. They are also key contributors to the pathogenesis of various neurodegenerative disorders, underscoring the need for in vitro models that accurately recapitulate disease-relevant conditions. Among the available isolation methods, the classical mixed glial culture shaking technique remains the most commonly employed, while alternatives such as magnetic bead separation and fluorescence-activated cell sorting (FACS) offer higher purity but are often constrained by technical complexity and cost. In this study, we refined the traditional shaking method by supplementing specific cytokines during culture to enhance microglial viability and proliferation. Our optimized protocol produced primary microglia with higher purity, greater yield, and improved viability compared with the conventional approach, thereby increasing experimental efficiency while substantially reducing time, animal usage, and overall cost.